added option to plot a triangular APA for submatrices extracted in rf mode.
HicAggR 1.1.2
minor fix in doc for preparePlotgardener
HicAggR 1.1.1
HicAggR is now on bioconductor release 3_19
added a minor fix to ExtractSubmatrix when using GRanges object to extract, retain only GRanges with seqnames that are present in hicList
added preparePlotgardener function to generate a data.frame that can be directly used in plotgardener’s plotHicTriangle, plotHicRectangle and plotHicSquare directly
HicAggR 0.99.7
caching in vignette
HicAggR 0.99.6
default set column names in OrientateMatrix are now removed, this is for ggAPA
ggAPA: “rf” mode has it’s own customized axes labels now
added introduction to the package’s vignette
HicAggR 0.99.5
added option to remove duplicated submatrices in SearchPairs
HicAggR 0.99.4
removed CITATION file
HicAggR 0.99.3
NAMESPACE was generated with roxygen2 to define exportable functions.
CompareToBackground: to correct the skewedness of o/e values towards long distances, computation of z.scores is now calculated using residuals from a polynomial model that fits the background couples (log(counts)~distance).
SearchPairs: added option to remove self interacting bins.
all internal functions are now in utilities.R.
Docs were reviewed.
HicAggR 0.99.2
Implemented import of corrected matrices for data in .hic and cool/mcool format.
Implemented import of O/E matrix for data in .hic format.
Implemented import of raw data in .h5 format.
Added GetInfo function to get info on a hic data (.hic, cool/mcool/h5 formats).
Removed dependency to BSDA::z.test in CompareToBackground.
Removed dependency to InteractionSet and added it as package to import in NAMESPACE to remove the PackageStartUpMessages.
Removed chatty package start up message and replaced it with nicer message.
Some BiocCheck NOTES were also takedn into consideration: changing sapply to vapply etc.
